-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/prep to search path.
-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib to search path.
-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm to search path.
-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source buildit-vac.in.

Welcome to LEaP!
Sourcing: ./buildit-vac.in
----- Source: ./leaprc.ff99bsc0
----- Source of ./leaprc.ff99bsc0 done
Log file: ./leap.log
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.parmbsc0
Reading force field modification type file (frcmod)
Reading title:
modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_nucleic94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_amino94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_aminoct94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/all_aminont94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/DNA_CI.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/ions94.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib
Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/RNA_CI.lib
Could not open file frcmod.tip3p: not found
Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: ./frcmod.ff99Chen-Garcia
Reading force field modification type file (frcmod)
Reading title:
glycosdic bond torsion modifications to parm99 from Chen and Garcia (PNAS, 2013, 110, 16820)
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.378936 angstroms between .R<RC3 2>.A<O4' 10> and .R<RC3 2>.A<H5'1 6>
Warning: Close contact of 0.666938 angstroms between .R<RC3 2>.A<C4' 8> and .R<RC3 2>.A<H5'1 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 3
Unit is OK.
Writing pdb file: init.pdb
	Quit